modules/vg_construct

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

vggraphconstructfastavcfstructural variants

https://github.com/nf-core/modules/[...]/modules/nf-core/vg/construct

Description

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`input:list`

Either one or more VCF files containing different contigs or a multiple sequence alignment file

*.{vcf.gz,fa,fasta,fna,clustal}

`tbis:list`

The index files for the VCF files

*.tbi

`insertions_fasta:file`

A FASTA file containing insertion sequences (referred to in the VCF file(s))

*.{fa,fasta,fna}

`meta2:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta:file`

The reference FASTA file (cannot be used in combination with msa, but is required when using vcfs)

*.{fa,fasta,fna}

`meta3:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta_fai:file`

The index of the reference FASTA file

*.fai

Output

name:type

description

pattern

`graph`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.vg:file`

The constructed graph

*.vg

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

vg
MIT

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

github.com/vgteam/vg github.com/vgteam/vg/wiki

modules/vg_construct

Description

Input

meta:map

input:list

tbis:list

insertions_fasta:file

meta2:map

fasta:file

meta3:map

fasta_fai:file

Output

graph

meta:map

*.vg:file

versions

versions.yml:file

Tools

vg MIT

`meta:map`

`input:list`

`tbis:list`

`insertions_fasta:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fasta_fai:file`

`graph`

`meta:map`

`*.vg:file`

`versions`

`versions.yml:file`

vg
MIT